Anomaly detection has an important impact on the development of unmanned aerial vehicles, and effective anomaly detection is fundamental to their utilization. Traditional anomaly detection discriminates anomalies for single-dimensional factors of sensing data, which often performs poorly in multidimensional data scenarios due to weak computational scalability and the problem of dimensional catastrophe, ignoring potential correlations between sensing data and some important information of certain characteristics. In order to capture the correlation of multidimensional sensing data and improve the accuracy of anomaly detection effectively, GTAF, an anomaly detection model for multivariate sequences based on an improved graph neural network with a transformer, a graph attention mechanism and a multi-channel fusion mechanism, is proposed in this paper. First, we added a multi-channel transformer structure for intrinsic pattern extraction of different data. Then, we combined the multi-channel transformer structure with GDN’s original graph attention network (GAT) to attain better capture of features of time series, better learning of dependencies between time series and hence prediction of future values of adjacent time series. Finally, we added a multi-channel data fusion module, which utilizes channel attention to integrate global information and upgrade anomaly detection accuracy. The results of experiments show that the average accuracies of GTAF, the anomaly detection model proposed in this paper, are 92.83% and 96.59% on two datasets from unmanned systems, respectively, which has higher accuracy and computational efficiency compared with other methods.